Artificial transcriptional terminators

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The goal is to create a series of transcriptional terminators with varying efficiencies. The majority of transcriptional terminators have a G+C rich stem of 7(+/-1)bp and a loop of 4(+/-1) nucleodtides followed by a poly(U) tail. Two common loops are UUCG and GAAA, both of which are known to increase RNA hairpin stability. The sequence GCGGG(G) is a common sequence found on the 3' arm of the stem. [1]

Contents

Effects of stem loop sequence on terminator efficiency

Bulges and mismatches in the stem, as well low G+C content of the stem will lower TE more than reducing the length of or elimination of the poly(U) tail [2]. The sequences downstream of the poly(U) tail and between the stop codon and the start of the stem loop structure also affect the TE of a terminator, particularly T7Te or T3Te.

T7Te

Several sources [3] [Chamberlin 79] measured the termination efficiency(TE) of T7Te at around 90%. However, efficiency for the biobricks part BBa_B0012 [1], also T7Te, is around 30%. T7Te has a very short poly(U) tail and requires the further downstream sequence for efficiecent termination [3], and this further downstream sequence is lacking in BBa_B0012. If the sequence for BBa_B0012 is lengthened to include this downstream segment, then the TE of part should be improved.

Predicting terminator efficiency

It may be possible to predict terminator efficiency using methods from d'Aubenton, in particular, the score d assigned to a possible terminator sequence

d = nt*18.16+Y*96.59-116.87

where nt measures the statistical distribution of the T residues in the non transcribed DNA strand and Y is the free energy per nucleodtide of the stem loop structure.

The score d will give a rough estimate of how efficient a terminator is.

d<0: TE<20%

0<d<30: 20%<TE<70%

d>30: TE>70%

Ideal terminator

has 6 base stem with 3' sequence of GCGGGG

4 base loop, either UUCG or GAAA

tail containing >8 uridines

for a biobrick part, flanking regions will be biobrick site

Designed terminators

The score d is calculated as mentioned above. The energy of hairpin formation, delG, is caluclated using UNAFold.

These terminators are designed to be bidirectional. delG reverse is the energy of hairpin formation on the opposite strand.

Terminator 1:

delG=-12.6 d=62.33 %T>90

delG reverse=-10.2 d=53.09 %T>90

stem loop: CCCCGCTTCGGCGGGG

primer 1: GTTTCTTCGAATTCGCGGCCGCTTCTAGAGAAAAAAAAACCCCGCTTCGGC

primer 2: GTTTCTTCCTGCAGCGGCCGCTACTAGTAAAAAAAAACCCCGCCGAAGC

Terminator 2:

delG=-12.6 d=38.25 %T>90

delG reverse=-10.2 d=23.02 %T=75

stem loop: CCCCGCTTCGGCGGGG

primer 1: GTTTCTTCGAATTCGCGGCCGCTTCTAGAGCGCAAAAAACCCCGCTTCGGC

primer 2: GTTTCTTCCTGCAGCGGCCGCTACTAGTAGCGAAAAAACCCCGCCGAAGC

Terminator 3:

delG=-12.6 d=27.78 %T=80

delG reverse=-10.2 d=11.64 %T=40

stem loop: CCCCGCTTCGGCGGGG

primer 1: GTTTCTTCGAATTCGCGGCCGCTTCTAGAGCGCCAAAAACCCCGCTTCGGC

primer 2: GTTTCTTCCTGCAGCGGCCGCTACTAGTAGCGGAAAAACCCCGCCGAAGC

Terminator 4:

delG=-12.6 d=16.05 %T=55

delG reverse=-10.2 d=0.91 %T=<20

stem loop: CCCCGCTTCGGCGGGG

primer 1: GTTTCTTCGAATTCGCGGCCGCTTCTAGAGGCCGAAAACCCCGCTTCGGC

primer 2: GTTTCTTCCTGCAGCGGCCGCTACTAGTACGGCAAAACCCCGCCGAAGC

Terminator 5:

delG=-12.6 d=4.22 %T=25

delG reverse=-10.2 d=-11 %T<10

stem loop: CCCCGCTTCGGCGGGG

primer 1: GTTTCTTCGAATTCGCGGCCGCTTCTAGAGCGCCGCAAACCCCGCTTCGGC

primer 2: GTTTCTTCCTGCAGCGGCCGCTACTAGTAGCGGCGAAACCCCGCCGAAGC

Terminator 6:

delG=-16.2 d=57.39 %T>90

delG reverse=-18.9 d=66.22 %T>90

stem loop: CCCCGCCCCUGACAGGGCGGGG

primer 1: GTTTCTTCGAATTCGCGGCCGCTTCTAGAGAAAAAAAAACCCCGCCCCTGACAGG

primer 2: GTTTCTTCCTGCAGCGGCCGCTACTAGTAAAAAAAAACCCCGCCCTGTCAGGG

Terminator 7:

delG=-16.2 d=33.32 %T=80

delG reverse=-18.9 d=42.69 %T>90

stem loop: CCCCGCCCCUGACAGGGCGGGG

primer 1: GTTTCTTCGAATTCGCGGCCGCTTCTAGAGCGCAAAAAACCCCGCCCCTGACAGG

primer 2: GTTTCTTCCTGCAGCGGCCGCTACTAGTAGCGAAAAAACCCCGCCCTGTCAGGG

Terminator 8:

delG=-16.2 d=22.84 %T=70

delG reverse=-18.9 d=33.03 %T=80

stem loop: CCCCGCCCCUGACAGGGCGGGG

primer 1: GTTTCTTCGAATTCGCGGCCGCTTCTAGAGCGCCAAAAACCCCGCCCCTGACAGG

primer 2: GTTTCTTCCTGCAGCGGCCGCTACTAGTAGCGGAAAAACCCCGCCCTGTCAGGG

Terminator 9:

delG=-16.2 d=11.56 %T=40

delG reverse=-18.9 d=22.31 %T=75

stem loop: CCCCGCCCCUGACAGGGCGGGG

primer 1: GTTTCTTCGAATTCGCGGCCGCTTCTAGAGCGCCGAAAACCCCGCCCCTGACAGG

primer 2: GTTTCTTCCTGCAGCGGCCGCTACTAGTAGCGGCAAAACCCCGCCCTGTCAGGG

Terminator 10:

delG=-16.2 d=-0.72 %T<10

delG reverse=-18.9 d=10.40 %T=40

stem loop: CCCCGCCCCUGACAGGGCGGGG

primer 1: GTTTCTTCGAATTCGCGGCCGCTTCTAGAGCGCCGCAAACCCCGCCCCTGACAGG

primer 2: GTTTCTTCCTGCAGCGGCCGCTACTAGTAGCGGCGAAACCCCGCCCTGTCAGGG

Terminator 11: this is not supposed to work. if it does, then something is wrong